a) Two true species trees used for simulating sequence data under the multispecies coalescent model. Parameters in the model include the three species divergence times (s) and the population size parameters (s) for the seven species. Each species is split into two populations in the species-delimitation analysis by bpp, with eight populations on the guide tree. Either three or five sequences are sampled from each populations, with either 24 or 40 sequences in the alignment at each locus. b) Two inferred population (guide) trees, with interior nodes labeled.

Frequency (out of 1000 replicates) at which each clade in the correct population (guide) tree is recovered by RAxML and *beast. The numbers above the branch are for the low-mutation rate while those below the branch are for the high rate. In each case, the three numbers are for RAxML for one mitochondrial locus, *beast with one nuclear locus, and *beast with five nuclear loci.

Frequency (out of 1000 replicates) at which each clade in the correct population (guide) tree is recovered by RAxML and beast in the analysis of the mitochondrial locus. The numbers above the branch are for the low-mutation rate whereas those below the branch are for the high rate. See legend to .

Histogram of posterior probabilities for splitting clades into different species by bpp in data of one locus, with three sequences sampled from each population at the locus, simulated using tree 1 at the low-mutation rate, when the guide tree was inferred using *beast. Each bin is of size 0.05. The frequencies in the last bin for splitting clades , and are the false-positive rates listed in .

Histogram of posterior probabilities for splitting the clades by bpp in data of five loci, with three sequences per population at each locus, simulated using tree 1 with low-mutation rate, when the guide tree was inferred using *beast. See legend to .